AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_fts_cell_wall_bbur_reg_300.orf -o250_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RBB00541 16 3615 RBB00440 35 3615 RBB00792 20 3615 Input sequences: #1 RBB00598 129 3615 #2 RBB00539 271 3615 #3 RBB00437 22 3615 #4 RBB00433 30 3615 #5 RBB00432 92 3615 #6 RBB00430 43 3615 #7 RBB00429 50 3615 #8 RBB00174 118 3615 #9 RBB00173 153 3615 #10 RBB00171 29 3615 #11 RBB00159 51 3615 #12 RBB00003 148 3615 #13 RBB00742 50 3615 #14 RBB00741 300 3615 #15 RBB00883 74 3615 #16 RBB00339 77 3615 #17 RBB00328 18 3615 Motif number 1 TGAAAAAGTAAATTACTATATAGCAGAGGGTA 1 15 0 AATATATATA 0.813632 -115 TGACTATATGAAATAAAAAATTATTCATTTTT 1 81 0 AATAAAAATT 0.915766 -49 ATTAAAGATAAATTAAAATAATACATAT 2 7 0 AATAAATAAT 0.854478 -265 ATTTTAATTTATCTTTAATAAAAATGCTTTAA 2 20 1 ATTTAATAAA 0.618655 -252 TTATGTCCTTAAGTATAAAAATATTTTTGACT 2 53 1 AATAAAAAAT 0.920387 -219 TTTATTAAAAAAATAGAAAATTGTAAATATAT 2 184 1 AATAAAAATT 0.916176 -88 AATAGCTAAGAAATTCAAAATTATGCTTCAAT 2 221 0 AATTAAAATT 0.862427 -51 TTTTACATAAAACTAATAAAAATAGCTAAGAA 2 241 0 AATATAAAAA 0.9013 -31 ACAAGTTATAAATTTATAAAAAACACCCT 5 8 0 AATTTAAAAA 0.575113 -85 TTAGCAAAAAATATATTAAATATTTTAACAAG 5 35 0 ATTATAAATA 0.813454 -58 TTTATCAGCTATCTAATATATTGATTTTAGCA 5 61 0 ATTATATATT 0.701394 -32 TATAATGAAAAAGTATAATAAAGTGTATTAAA 7 20 1 AATAAATAAA 0.847127 -31 ATTATTTAATTATAATATATTTTAGTATA 8 8 1 AATAAATATA 0.839086 -111 TTATAATATATTTTAGTATAATTAATAGTTAA 8 20 1 TTTATATAAT 0.488417 -99 AATTAATAGTTAATTCTAAATATATGTATATT 8 39 1 TATTTAAATA 0.655555 -80 ATTTAATCCAATCTAGAATATACATATATTTA 8 55 0 ATTAAATATA 0.725796 -64 ATTTAGTTAAAAGTAATAAATAAAGGAGACTG 8 85 1 AATATAAATA 0.895806 -34 ATTGCTTTCAAATTAGTATAATCAGAATGAAT 9 73 0 AATATATAAT 0.831008 -81 ACATTTCTCAAAATTGAAAAAATAAAAAATCT 11 11 1 AATTAAAAAA 0.863117 -41 ACGTACTTAATAATAAATTAGATTTTTTA 11 33 0 TATATAAATT 0.77746 -19 AATTGATTCAATCTTAAAAATTGAATTTAATG 12 21 0 ATTTAAAATT 0.726506 -128 TATTGCAATATATTATTAAAATAAAATGTGAA 12 76 1 TATATAAAAT 0.767117 -73 AGCATTTACTTTGTAATAAATTTTTTCACATT 12 100 0 TTTATAAATT 0.639281 -49 CGCAAAGCATATCTTCAAAAATTTCTTCTACT 14 50 0 ATTTAAAAAT 0.772177 -251 ATTTACAATCAATTACAAAAAAGTAAATAATT 14 135 1 AATAAAAAAA 0.916008 -166 AAAAAGTAAATAATTCAAAAAATACTCCCCCT 14 152 1 TATTAAAAAA 0.707322 -149 TGTGCCAATTTAATTTAAAAATGGTTTTAAAC 14 208 0 TATTAAAAAT 0.700683 -93 CATGGAAATTAAGTAGTAAAAACTTAATCACA 14 247 1 AATATAAAAA 0.901379 -54 TTTCTCCCCTTTCTTGAATATTGTGATTAAGT 14 268 0 TTTTAATATT 0.383274 -33 ATAATATATATTATATAATATACATTA 15 6 1 ATTATATATA 0.688786 -69 ATTATATTTGAATTTATAAATTTTGATGTCCT 15 34 1 AATTTAAATT 0.487321 -41 GAAAATCTAAAAATAAAAAAATATCAATAATG 16 30 0 AATAAAAAAT 0.920429 -48 TTTTTAGATTTTCTTAAAAAAAGAAATAGAGG 16 49 1 TTTTAAAAAA 0.54563 -29 ** ** ****** Masking position 8 Map Score: 31.632 Number of sites scoring better than the average of aligned sites = 5329 Number in coding regions = 3264 Number in noncoding regions = 2065 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 2 CTATATTATTATATGTTATTATATTCTGAAAAAGT 1 38 0 ATGATATATT 0.515185 -92 ATTTTTATTAAAGATAAATTAAAATAATACATAT 2 10 0 AATATAAAAT 0.712041 -262 CTTCTAAGATCAAGTCAAAAATATTTTTATACTTA 2 62 0 CATAAATATT 0.898335 -210 AAAAATAGAAAATTGTAAATATATTTTCTATTGAA 2 192 1 AAGAAATATT 0.862133 -80 AACTAATAAAAATAGCTAAGAAATTCAAAATTATG 2 228 0 AAGAAAAATT 0.833866 -44 AACTTGTTAAAATATTTAATATATTTTTTGCTAAA 5 33 1 AATAAATATT 0.771189 -60 CAAATTAATCAAATTGTTATAAACA 6 1 1 CATATAAATT 0.836384 -43 TTATAATGAAAAAGTATAATAAAGTGTATTAAAGG 7 19 1 AATAAAAAGT 0.764141 -32 ACTATTAATTATACTAAAATATATTATAATTAAAT 8 14 0 ATTAAATATT 0.802664 -105 TGATTATACTAATTTGAAAGCAATTCCTTTTGCTT 9 81 1 AATAACAATT 0.854761 -73 ACATTTCTCAAAATTGAAAAAATAAAAAATCTAA 11 10 1 AATAAAAATA 0.654218 -42 GAAAAAATAAAAAATCTAATTTATTATTAAGTACG 11 26 1 AATAATTATT 0.653794 -26 ATTTAAATTCCATTAAATTCAATTTTTAA 12 5 1 AATATAAATT 0.935138 -144 TTCAATTTTTAAGATTGAATCAATTTCTTGGTACA 12 28 1 AATAACAATT 0.940298 -121 GGAAATACTGATATTGCAATATATTATTAAAATAA 12 65 1 ATTAAATATT 0.802657 -84 TATTAAAATAAAATGTGAAAAAATTTATTACAAAG 12 89 1 AAGAAAAATT 0.949444 -60 AAACGGAGGCCAAGTAGAAGAAATTTTTGAAGATA 14 38 1 CATAAAAATT 0.919404 -263 TTTGCGAACAAAGAGCAAAACAAATGGCACAAGCT 14 76 1 AAGAACAAAT 0.611811 -225 TTGCCGATTTAATTTACAATCAATTACAAAAAAGT 14 124 1 AATAACAATT 0.935918 -177 CCTAAACTCAAAATTATATCCTATTTAGTTTAAAA 14 181 1 AATATCTATT 0.842705 -120 TATATTATATAATATACATTATATTTGAATTTATA 15 17 1 AATATATATT 0.912226 -58 AACCTTAACAAAAGGACATCAAAATTTATAAATTC 15 43 0 AAGATAAAAT 0.590887 -32 AGCAAGTAAAAGATATTT 17 3 1 CATAAATATT 0.898335 -16 ** * ** ***** Masking position 8 Map Score: 22.8508 Number of sites scoring better than the average of aligned sites = 1648 Number in coding regions = 1103 Number in noncoding regions = 545 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 3 GCTATATAGTAATTTACTTTTTCAGAATATA 1 23 1 AATTTATTTT 0.875087 -107 ATATGTATTATTTTAATTTATCTTTAATAA 2 10 1 ATTTTATTTA 0.927825 -262 AACTTAAAGCATTTTTATTAAAGATAAATTA 2 24 0 ATTTTTTTAA 0.685898 -248 TACAATTTTCTATTTTTTTAATAAACTAAGC 2 178 0 TATTTTTTAA 0.679638 -94 CTATCTAATATATTGATTTTAGCAAAAAATA 5 54 0 TATTGATTTA 0.866383 -39 ATTATTTAATTATAATATATTTT 8 3 1 TATTTATTAT 0.679638 -116 GATTGGATTAAATTTAGTTAAAAGTAATAAA 8 74 1 AATTTATTAA 0.875087 -45 AGGTTCCGGTATTTGTCTTTACAAAAATCTT 9 122 1 ATTTGTTTTA 0.733389 -32 CAAAAATCTTAATTTTTTTAT 9 143 1 AATTTTTTAT 0.543382 -11 TAAATTAGATTTTTTATTTTTTCAATTTTGA 11 18 0 TTTTTATTTT 0.795622 -34 CAATCTTAAAAATTGAATTTAATGGAATTTA 12 14 0 AATTGATTTA 0.898218 -135 ATTTTTTCACATTTTATTTTAATAATATATT 12 82 0 ATTTTATTTA 0.927825 -67 ATTTTTATTTACTCATGAAAA 12 138 0 ATTTTTTTTA 0.841227 -11 TGGCCTTGCCGATTTAATTTACAATCAATTA 14 119 1 GATTTATTTA 0.843016 -182 TTTTTTGAATTATTTACTTTTTTGTAATTGA 14 143 0 TATTTATTTT 0.837328 -158 TAGGATATAATTTTGAGTTTAGGGGGAGTAT 14 173 0 TTTTGATTTA 0.83062 -128 AATTATATCCTATTTAGTTTAAAACCATTTT 14 192 1 TATTTATTTA 0.925866 -109 AAACTGTGCCAATTTAATTTAAAAATGGTTT 14 213 0 AATTTATTTA 0.944437 -88 TATACATTATATTTGAATTTATAAATTTTGA 15 29 1 ATTTGATTTA 0.869694 -46 TATTGATATTTTTTTATTTTTAGATTTTCTT 16 33 1 TTTTTATTTT 0.795622 -45 TTTATTTTTAGATTTTCTTAAAAAAAGAAAT 16 45 1 GATTTTTTAA 0.477041 -33 ****** **** Masking position 4 Map Score: 23.2621 Number of sites scoring better than the average of aligned sites = 2118 Number in coding regions = 1288 Number in noncoding regions = 830 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 4 ATAACATATAATAATATAGATGCAAAAAAAAATGAA 1 54 1 ATAATTGCAA 0.902079 -76 ATATGTATTATTTTAATTTATCTTTA 2 1 1 ATTTATTTAA 0.357763 -271 AGCTATTTTTATTAGTTTTATGTAAAATTTTAATGT 2 246 1 ATATTTGTAA 0.895045 -26 TTTTTTATAAATTTATAACTTGTTAAAATATTTAAT 5 17 1 ATTTATGTAA 0.827458 -76 AAAATATTTAATATATTTTTTGCTAAAATCAATATA 5 41 1 ATTTTTGCAA 0.902361 -52 AAATCAATATATTAGATAGCTGATAAATCACCCTTT 5 66 1 ATAATTGAAA 0.757403 -27 CAAATTAATCAAATTGTTATAAACAGATTTAAA 6 8 1 ATAATTATAA 0.451328 -36 ATTTTATACCTTTAAATCTGTTTATA 6 28 0 ATTATTTTAA 0.683194 -16 GGATAGCGTGATATATTTAGTGTTAATAAAGATTTT 9 16 1 ATTTTTGTAA 0.926394 -138 ATAAAAAAATTAAGATTTTTGTAAAGACAAATACC 9 129 0 TTAATTGTAA 0.805297 -25 AATAAAATTATATCAAACCTGCCAACTGT 10 5 0 ATTAATGCAA 0.838587 -25 ACATTTCTCAAAATTGAAAAAATAAAAAAT 11 5 1 TTTAATGAAA 0.320528 -47 AGACCAGAACATGTCATGAATGTCAATG 13 3 0 ATTATTGTAA 0.927114 -48 GTTTAGCAAATTTTGATCTTTGTTAAGAGTT 14 6 0 TTTATTGTAA 0.870085 -295 TTTTTACTACTTAATTTCCATGCAAAAACTGTGCCA 14 233 0 TTATTTGCAA 0.704534 -68 ** * ** *** ** Masking position 15 Map Score: 6.20244 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 456 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 GAAAAAGTAAATTACTATATAGCAGAGGGT 1 16 0 ATTACTATAT 0.509872 -114 ATTATTATATGTTATTATATTCTGAAAAAG 1 39 0 GTTATTATAT 0.571117 -91 TTGCATCTATATTATTATATGTTATTATAT 1 49 0 ATTATTATAT 0.796269 -81 GACCTCTTAAATTATTTTATGACTATATGA 1 102 0 ATTATTTTAT 0.555183 -28 TATGTATTATTTTAATTTATCTTTAATAAA 2 12 1 TTTAATTTAT 0.406832 -260 GTCCTTAAGTATAAAAATATTTTTGACTTG 2 57 1 ATAAAAATAT 0.510072 -215 ATAGAAAATTGTAAATATATTTTCTATTGA 2 196 1 GTAAATATAT 0.787285 -76 TTCTCCCCACCTTAATTTAT 4 1 0 CTTAATTTAT 0.585379 -30 GGTGTTTTTTATAAATTTATAACTTGTTAA 5 13 1 ATAAATTTAT 0.47795 -80 GATTTTAGCAAAAAATATATTAAATATTTT 5 41 0 AAAAATATAT 0.895626 -52 TTTTGCTAAAATCAATATATTAGATAGCTG 5 58 1 ATCAATATAT 0.613875 -35 AAAATATATTATAATTAAATAAT 8 4 0 ATAATTAAAT 0.31238 -115 TTAATTATACTAAAATATATTATAATTAAA 8 15 0 TAAAATATAT 0.650987 -104 ATAGTTAATTCTAAATATATGTATATTCTA 8 44 1 CTAAATATAT 0.829299 -75 TTTATTAACACTAAATATATCACGCTATCC 9 16 0 CTAAATATAT 0.829299 -138 AATAAAATTATATCAAACCTGCC 10 17 0 AAAATTATAT 0.784597 -13 ACGTACTTAATAATAAATTAGATTTTTT 11 34 0 AATAATAAAT 0.420776 -18 ATTTTATTTTAATAATATATTGCAATATCA 12 73 0 AATAATATAT 0.879919 -76 TAAAATGTGAAAAAATTTATTACAAAGTAA 12 97 1 AAAAATTTAT 0.717187 -52 CCCTAAACTCAAAATTATATCCTATTTAGT 14 180 1 AAAATTATAT 0.784597 -121 AGTTATTATATTTTCTCCCCT 14 290 0 GTTATTATAT 0.571117 -11 ATGTATATTATATAATATATATTAT 15 6 0 TATAATATAT 0.613149 -69 AAAAGGACATCAAAATTTATAAATTCAAAT 15 39 0 CAAAATTTAT 0.570056 -36 AAAAAATATCAATAATGTATCAAGTTTTAC 16 17 0 AATAATGTAT 0.437352 -61 ATCTAAAAATAAAAAAATATCAATAATGTA 16 28 0 AAAAAAATAT 0.460801 -50 ********** Masking position 10 Map Score: 17.7947 Number of sites scoring better than the average of aligned sites = 1384 Number in coding regions = 819 Number in noncoding regions = 565 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 6 AAGTGTATTAAAGGGATTGAT 7 40 1 AAGGATTGAT 0.885918 -11 ATTTAGTTAAAAGTAATAAATAAAGGAGACT 8 85 1 AAGAATAAAT 0.807091 -34 AATAAAGCAAAAGGAATTGCTTTCAAATTAG 9 89 0 AAGAATTGCT 0.966282 -65 CCTTTGTACCAAGAAATTGATTCAATCTTAA 12 36 0 AAGAATTGAT 0.966926 -113 TCTTGGTACAAAGGAAATACTGATATTGCAA 12 53 1 AAGAAATACT 0.918046 -96 ATTTATTACAAAGTAAATGCTTTATTGTTTT 12 111 1 AAGAAATGCT 0.966282 -38 AATTACAAAAAAGTAAATAATTCAAAAAATA 14 145 1 AAGAAATAAT 0.91954 -156 AGCAAGTAAAAGATATTT 17 4 1 AAGAAAAGAT 0.914554 -15 *** ******* Masking position 6 Map Score: 6.1944 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 57 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ********** No masking Map Score: 1.28851e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 1.28851e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: 1.28851e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0